Physiology and ecology of ammonia-oxidizing Archaea

在海洋浮游微生物群落中，海洋新考古动物群占了很大一部分(高达40%)。最近在纯培养中分离到了丰富的海洋类群1中的第一个培养成员--Candidatus Nitrosopumilus maritimus，首次在Archaea域中显示了硝化作用。像已知的细菌氨氧化菌一样，N.maritmus通过好氧将氨转化为亚硝酸盐，并固定无机碳进行生物合成。这一建议的第一个目的是了解唯一存在的纯培养物的化学自养生命所涉及的生化途径。这些研究将与华盛顿大学的大卫·斯塔尔密切合作，并由联合基因组研究所正在进行的全基因组分析提供便利。我们的部分将是对参与碳代谢的酶进行生化和微生物分析，并批准假设的途径。将进行示踪实验，以确定maritimus是严格的自养还是混养。对黑线姬松茸生长过程中碳同位素分馏的测定将为固碳途径提供信息。利用海绵共生体的环境基因组学研究，将在海洋新月形藻中证明存在一个用于固定二氧化碳的改良的3-羟基丙酸循环。拟议项目的第二个目标是分析自然环境中预测的古氨氧化菌的高丰度和多样性。此前对16S rRNA和amoA基因的分析表明，这一组基因普遍存在。然而，目前尚不清楚其成员是否在体内氧化氨。这两个基因的系统发育多样性表明存在不同的生理学类型。在我们的项目中，我们将从检测到相应生物标志物的水生和陆地环境中分离出更多的菌株。新的菌株将具有生理学特征，并将有助于理解所提出的对生物地球化学氮和碳循环的高度影响。

Marine Crenarchaeota have been found to represent a major fraction (up to 40 %) of the planktonic microbial community in the Ocean. The first cultured member of the abundant marine group 1 Crenarchaeota, candidatus Nitrosopumilus maritimus, was recently isolated into pure culture, showing for the first time nitrification among the domain Archaea. Like known bacterial ammonia oxidizers, N. maritmus converts aerobically ammonia to nitrite and fixes inorganic carbon for biosynthesis. The first aim of this proposal is to understand the biochemical pathways involved in the chemolithoautotrophic life of the only existing pure culture. The studies will be performed in close collaboration with David Stahl at the University of Washington and facilitated by the ongoing whole genome analysis at the Joint Genome Institute. Our part will be the biochemical and microbiological analysis of enzymes involved in the carbon metabolism and the approval of hypothetical pathways. Tracer experiments will be performed to determine if N. maritimus is either strict autotroph or mixotroph. Determination of the carbon isotope fractionation during growth of N. maritimus will provide information on the carbon fixation pathway. The existence of a modified 3-hydroxypropionate cycle for CO2 fixation derived from environmental genomics of crenarchaeal sponge symbionts will be proven biochemically in N. maritimus. The second goal of the proposed project is to analyze the predicted high abundance and diversity of crenarchaeal ammonia oxidizers in natural environments. Previous analyses of 16S rRNA and amoA genes have indicated a ubiquitous distribution of this group. However, it is unclear whether its members are oxidizing ammonia in vivo. The phylogenetic diversity of both genes suggests the existence of various physiotypes. In our project we will isolate further strains from aquatic and terrestrial environments where the corresponding biomarkers have been detected. The new strains will be characterized physiologically and will help to understand the suggested high impact on the biogeochemical nitrogen and carbon cycles.